[quote name='SourTaxi']I ordered the game last week and it came with both.
I think Gamefly usually gives you whatever you would have gotten if you bought it new.[/QUOTE]
^This is true, always. GameFly always gives you whatever's in the case, completely unused: the case itself, instruction book, DLC codes, etc.
I haven't bought a 3DS game from them before, but I'd be willing to bet it's exactly the same as when I bought PS3 games from them (many times).